Starting phenix.real_space_refine on Sat Sep 12 10:44:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d33_27154/09_2026/8d33_27154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d33_27154/09_2026/8d33_27154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d33_27154/09_2026/8d33_27154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d33_27154/09_2026/8d33_27154.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d33_27154/09_2026/8d33_27154.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d33_27154/09_2026/8d33_27154.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d33_27154/09_2026/8d33_27154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d33_27154/09_2026/8d33_27154.map" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.325 sd= 0.631 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 49 5.49 5 S 82 5.16 5 C 9585 2.51 5 N 2683 2.21 5 O 2872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15272 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3213 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.65, per 1000 atoms: 0.24 Number of scatterers: 15272 At special positions: 0 Unit cell: (107.1, 124.95, 153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 82 16.00 P 49 15.00 O 2872 8.00 N 2683 7.00 C 9585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 692.9 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 48.3% alpha, 14.1% beta 22 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.860A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.115A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.523A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 5.242A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.835A pdb=" N GLN A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.677A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 786 through 810 removed outlier: 5.079A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.712A pdb=" N GLN A 922 " --> pdb=" O TRP A 918 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 923 " --> pdb=" O MET A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 955 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 987 removed outlier: 3.750A pdb=" N MET A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.616A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.572A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1174 through 1178 removed outlier: 3.589A pdb=" N VAL A1177 " --> pdb=" O PRO A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 165 through 178 removed outlier: 3.877A pdb=" N ALA B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 193 No H-bonds generated for 'chain 'B' and resid 192 through 193' Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.580A pdb=" N ASP B 198 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 266 removed outlier: 3.784A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.500A pdb=" N LYS B 321 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.638A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.657A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.508A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 483 removed outlier: 4.492A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 150 through 155 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 166 through 178 removed outlier: 3.638A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.110A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.566A pdb=" N THR C 420 " --> pdb=" O TYR C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.718A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 450 " --> pdb=" O THR C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 485 removed outlier: 4.610A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.910A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N SER A 216 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ALA A 194 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AA3, first strand: chain 'A' and resid 747 through 751 Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 6.688A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.379A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 148 removed outlier: 4.037A pdb=" N GLY C 179 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.405A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.182A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB3, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.176A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4795 1.34 - 1.46: 3021 1.46 - 1.58: 7714 1.58 - 1.70: 91 1.70 - 1.82: 130 Bond restraints: 15751 Sorted by residual: bond pdb=" O5' DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.579 1.805 -0.226 1.50e-02 4.44e+03 2.28e+02 bond pdb=" C5' DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 1.443 1.323 0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.592 1.707 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 1.600 1.650 -0.050 1.10e-02 8.26e+03 2.10e+01 bond pdb=" C4 DCP A1302 " pdb=" N4 DCP A1302 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.20e-02 6.94e+03 2.06e+01 ... (remaining 15746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 21483 3.38 - 6.76: 54 6.76 - 10.14: 6 10.14 - 13.52: 2 13.52 - 16.90: 2 Bond angle restraints: 21547 Sorted by residual: angle pdb=" O2B DCP A1302 " pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 106.94 123.84 -16.90 1.88e+00 2.83e-01 8.08e+01 angle pdb=" O2A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " ideal model delta sigma weight residual 106.94 123.75 -16.81 1.88e+00 2.83e-01 8.00e+01 angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 132.92 6.95 1.00e+00 1.00e+00 4.83e+01 angle pdb=" O2G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 104.48 97.94 6.54 1.14e+00 7.76e-01 3.32e+01 angle pdb=" C1' DCP A1302 " pdb=" N1 DCP A1302 " pdb=" C6 DCP A1302 " ideal model delta sigma weight residual 121.66 114.58 7.08 1.39e+00 5.21e-01 2.61e+01 ... (remaining 21542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8601 17.84 - 35.68: 474 35.68 - 53.52: 146 53.52 - 71.36: 35 71.36 - 89.20: 12 Dihedral angle restraints: 9268 sinusoidal: 4121 harmonic: 5147 Sorted by residual: dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 130.66 -37.66 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA LEU A 195 " pdb=" C LEU A 195 " pdb=" N VAL A 196 " pdb=" CA VAL A 196 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLU A 181 " pdb=" C GLU A 181 " pdb=" N GLY A 182 " pdb=" CA GLY A 182 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 9265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1727 0.037 - 0.074: 399 0.074 - 0.111: 106 0.111 - 0.149: 79 0.149 - 0.186: 11 Chirality restraints: 2322 Sorted by residual: chirality pdb=" C3' DG T 10 " pdb=" C4' DG T 10 " pdb=" O3' DG T 10 " pdb=" C2' DG T 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" C3' DG T 5 " pdb=" C4' DG T 5 " pdb=" O3' DG T 5 " pdb=" C2' DG T 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C3' DC P 10 " pdb=" C4' DC P 10 " pdb=" O3' DC P 10 " pdb=" C2' DC P 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 2319 not shown) Planarity restraints: 2602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 452 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C TYR A 452 " 0.022 2.00e-02 2.50e+03 pdb=" O TYR A 452 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 453 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 21 " -0.015 2.00e-02 2.50e+03 7.52e-03 1.27e+00 pdb=" N1 DC T 21 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC T 21 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC T 21 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC T 21 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC T 21 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC T 21 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC T 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC T 21 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 482 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 483 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " 0.015 5.00e-02 4.00e+02 ... (remaining 2599 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 200 2.65 - 3.21: 13847 3.21 - 3.78: 23198 3.78 - 4.34: 32745 4.34 - 4.90: 52114 Nonbonded interactions: 122104 Sorted by model distance: nonbonded pdb=" OE2 GLU B 165 " pdb=" NZ LYS C 160 " model vdw 2.091 3.120 nonbonded pdb=" O THR B 460 " pdb=" OG1 THR B 461 " model vdw 2.095 3.040 nonbonded pdb=" OG SER A1230 " pdb=" OE1 GLU A1232 " model vdw 2.105 3.040 nonbonded pdb=" O PRO A 217 " pdb=" OG SER A 218 " model vdw 2.125 3.040 nonbonded pdb=" O THR C 460 " pdb=" OG1 THR C 461 " model vdw 2.130 3.040 ... (remaining 122099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 355 or resid 368 through 485)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.110 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.226 15752 Z= 0.278 Angle : 0.572 16.903 21549 Z= 0.365 Chirality : 0.042 0.186 2322 Planarity : 0.003 0.027 2602 Dihedral : 13.120 89.196 5943 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 0.39 % Allowed : 4.39 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1758 helix: 1.34 (0.20), residues: 739 sheet: 0.94 (0.31), residues: 242 loop : -0.16 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.009 0.001 TYR A1108 PHE 0.014 0.001 PHE A 197 TRP 0.006 0.001 TRP A 220 HIS 0.002 0.001 HIS C 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.28 (15751) covalent geometry : angle 0.57178 / 0.36 (21547) SS BOND : bond 0.00604 / 0.32 ( 1) SS BOND : angle 0.99494 / 0.56 ( 2) hydrogen bonds : bond 0.15236 / 10.20 ( 733) hydrogen bonds : angle 6.12378 / 4.38 ( 1999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 488 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 VAL cc_start: 0.8762 (p) cc_final: 0.8499 (t) REVERT: A 877 MET cc_start: 0.7530 (mmm) cc_final: 0.7325 (mmt) REVERT: A 993 ARG cc_start: 0.6388 (tpp-160) cc_final: 0.6020 (tpm-80) REVERT: A 1095 SER cc_start: 0.7752 (m) cc_final: 0.7477 (t) REVERT: B 257 ARG cc_start: 0.7323 (mtp-110) cc_final: 0.6973 (mtp-110) REVERT: B 310 GLU cc_start: 0.7841 (mp0) cc_final: 0.7493 (mp0) REVERT: B 462 MET cc_start: 0.8512 (mmm) cc_final: 0.8263 (mmm) REVERT: C 129 ASP cc_start: 0.7081 (t70) cc_final: 0.6837 (t0) REVERT: C 455 LEU cc_start: 0.8316 (tt) cc_final: 0.8090 (tp) outliers start: 6 outliers final: 1 residues processed: 492 average time/residue: 0.6258 time to fit residues: 337.2261 Evaluate side-chains 386 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1098 ASN A1157 ASN A1175 GLN B 187 HIS B 195 ASN B 339 ASN B 409 ASN C 166 GLN C 339 ASN C 400 GLN C 409 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.113564 restraints weight = 25995.979| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.40 r_work: 0.3542 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 15752 Z= 0.282 Angle : 0.778 9.143 21549 Z= 0.416 Chirality : 0.051 0.190 2322 Planarity : 0.007 0.071 2602 Dihedral : 14.132 63.448 2436 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 4.39 % Allowed : 14.86 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1758 helix: 1.01 (0.19), residues: 744 sheet: 1.01 (0.31), residues: 231 loop : -0.51 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 203 TYR 0.021 0.003 TYR C 206 PHE 0.036 0.003 PHE A 197 TRP 0.012 0.003 TRP C 262 HIS 0.006 0.002 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.28 (15751) covalent geometry : angle 0.77793 / 0.42 (21547) SS BOND : bond 0.00910 / 0.48 ( 1) SS BOND : angle 1.13884 / 0.66 ( 2) hydrogen bonds : bond 0.07049 / 4.87 ( 733) hydrogen bonds : angle 5.05575 / 3.57 ( 1999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 360 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 VAL cc_start: 0.8692 (p) cc_final: 0.8428 (t) REVERT: A 546 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8231 (ttm170) REVERT: A 877 MET cc_start: 0.7511 (mmm) cc_final: 0.7293 (mmt) REVERT: A 963 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: A 993 ARG cc_start: 0.6439 (tpp-160) cc_final: 0.6217 (tpm-80) REVERT: A 1102 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: A 1138 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8550 (mmt180) REVERT: B 134 LYS cc_start: 0.8432 (tptp) cc_final: 0.8190 (tttp) REVERT: B 310 GLU cc_start: 0.7990 (mp0) cc_final: 0.7594 (mp0) REVERT: C 86 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6543 (mm) REVERT: C 129 ASP cc_start: 0.7182 (t70) cc_final: 0.6855 (t0) outliers start: 68 outliers final: 39 residues processed: 397 average time/residue: 0.6009 time to fit residues: 262.4228 Evaluate side-chains 384 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 340 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 776 ASP Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 963 GLU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1222 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 149 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 82 optimal weight: 0.0030 chunk 38 optimal weight: 5.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN B 404 ASN C 249 ASN C 339 ASN C 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.116530 restraints weight = 26194.472| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.40 r_work: 0.3590 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15752 Z= 0.140 Angle : 0.609 9.238 21549 Z= 0.325 Chirality : 0.043 0.168 2322 Planarity : 0.005 0.041 2602 Dihedral : 14.182 62.326 2436 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 3.42 % Allowed : 17.89 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1758 helix: 1.52 (0.19), residues: 743 sheet: 1.15 (0.30), residues: 248 loop : -0.31 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 628 TYR 0.016 0.002 TYR A 150 PHE 0.024 0.002 PHE A 197 TRP 0.015 0.001 TRP A 897 HIS 0.003 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (15751) covalent geometry : angle 0.60851 / 0.32 (21547) SS BOND : bond 0.00367 / 0.19 ( 1) SS BOND : angle 0.54723 / 0.32 ( 2) hydrogen bonds : bond 0.05090 / 3.54 ( 733) hydrogen bonds : angle 4.62196 / 3.26 ( 1999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 368 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7189 (pmt170) cc_final: 0.6627 (pmt170) REVERT: A 543 VAL cc_start: 0.8655 (p) cc_final: 0.8398 (t) REVERT: A 877 MET cc_start: 0.7496 (mmm) cc_final: 0.7276 (mmt) REVERT: A 1138 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8481 (mmt180) REVERT: B 134 LYS cc_start: 0.8390 (tptp) cc_final: 0.8154 (tttp) REVERT: B 310 GLU cc_start: 0.7909 (mp0) cc_final: 0.7521 (mp0) REVERT: C 86 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6573 (mm) outliers start: 53 outliers final: 27 residues processed: 395 average time/residue: 0.5727 time to fit residues: 249.0049 Evaluate side-chains 379 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 350 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 157 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 277 HIS A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN C 409 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114267 restraints weight = 26129.397| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.40 r_work: 0.3554 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15752 Z= 0.214 Angle : 0.696 10.658 21549 Z= 0.370 Chirality : 0.047 0.164 2322 Planarity : 0.006 0.054 2602 Dihedral : 14.397 62.586 2436 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 4.52 % Allowed : 18.67 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.20), residues: 1758 helix: 1.26 (0.19), residues: 744 sheet: 1.07 (0.30), residues: 241 loop : -0.47 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 264 TYR 0.017 0.002 TYR A 150 PHE 0.029 0.002 PHE A 197 TRP 0.014 0.002 TRP A1049 HIS 0.004 0.001 HIS A 932 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (15751) covalent geometry : angle 0.69624 / 0.37 (21547) SS BOND : bond 0.00694 / 0.37 ( 1) SS BOND : angle 0.91624 / 0.52 ( 2) hydrogen bonds : bond 0.06057 / 4.21 ( 733) hydrogen bonds : angle 4.79711 / 3.39 ( 1999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 352 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 877 MET cc_start: 0.7536 (mmm) cc_final: 0.7318 (mmt) REVERT: A 1138 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8478 (mmt180) REVERT: B 134 LYS cc_start: 0.8387 (tptp) cc_final: 0.8153 (tttp) REVERT: B 310 GLU cc_start: 0.7933 (mp0) cc_final: 0.7541 (mp0) REVERT: C 86 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6621 (mm) outliers start: 70 outliers final: 42 residues processed: 395 average time/residue: 0.5676 time to fit residues: 246.6678 Evaluate side-chains 388 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 344 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 179 optimal weight: 9.9990 chunk 44 optimal weight: 0.0060 chunk 150 optimal weight: 0.1980 chunk 174 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN B 305 ASN B 339 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115368 restraints weight = 26188.104| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.41 r_work: 0.3574 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15752 Z= 0.155 Angle : 0.638 10.172 21549 Z= 0.337 Chirality : 0.043 0.164 2322 Planarity : 0.005 0.044 2602 Dihedral : 14.414 61.766 2436 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 4.84 % Allowed : 18.99 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1758 helix: 1.44 (0.19), residues: 743 sheet: 1.13 (0.30), residues: 247 loop : -0.40 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 628 TYR 0.016 0.002 TYR A 150 PHE 0.023 0.002 PHE A 197 TRP 0.017 0.001 TRP A 175 HIS 0.003 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (15751) covalent geometry : angle 0.63831 / 0.34 (21547) SS BOND : bond 0.00459 / 0.24 ( 1) SS BOND : angle 0.66367 / 0.38 ( 2) hydrogen bonds : bond 0.05236 / 3.64 ( 733) hydrogen bonds : angle 4.64630 / 3.28 ( 1999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 345 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: A 309 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7445 (mpp80) REVERT: A 877 MET cc_start: 0.7522 (mmm) cc_final: 0.7297 (mmt) REVERT: A 1138 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8477 (mmt180) REVERT: B 134 LYS cc_start: 0.8365 (tptp) cc_final: 0.8134 (tttp) REVERT: C 86 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6614 (mm) outliers start: 75 outliers final: 41 residues processed: 393 average time/residue: 0.5780 time to fit residues: 250.1951 Evaluate side-chains 382 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 337 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 2.9990 chunk 130 optimal weight: 0.0170 chunk 75 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN C 249 ASN C 339 ASN C 400 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.125948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.117584 restraints weight = 26271.571| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.41 r_work: 0.3608 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15752 Z= 0.122 Angle : 0.598 10.626 21549 Z= 0.315 Chirality : 0.041 0.162 2322 Planarity : 0.004 0.044 2602 Dihedral : 14.345 60.561 2436 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 3.94 % Allowed : 20.22 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1758 helix: 1.67 (0.19), residues: 745 sheet: 1.37 (0.30), residues: 250 loop : -0.31 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1096 TYR 0.015 0.001 TYR A1166 PHE 0.021 0.001 PHE C 254 TRP 0.022 0.001 TRP A 175 HIS 0.003 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (15751) covalent geometry : angle 0.59826 / 0.31 (21547) SS BOND : bond 0.00312 / 0.16 ( 1) SS BOND : angle 0.44651 / 0.26 ( 2) hydrogen bonds : bond 0.04385 / 3.05 ( 733) hydrogen bonds : angle 4.44831 / 3.15 ( 1999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 357 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: A 539 PHE cc_start: 0.8247 (t80) cc_final: 0.8013 (t80) REVERT: A 877 MET cc_start: 0.7493 (mmm) cc_final: 0.7268 (mmt) REVERT: A 1054 GLU cc_start: 0.6906 (mp0) cc_final: 0.6672 (mp0) REVERT: B 134 LYS cc_start: 0.8352 (tptp) cc_final: 0.8127 (tttp) REVERT: B 158 GLN cc_start: -0.2819 (OUTLIER) cc_final: -0.3430 (mt0) REVERT: B 310 GLU cc_start: 0.8005 (mp0) cc_final: 0.7597 (mp0) REVERT: C 86 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6577 (mm) outliers start: 61 outliers final: 30 residues processed: 395 average time/residue: 0.5840 time to fit residues: 254.2197 Evaluate side-chains 379 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 346 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 153 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 45 optimal weight: 0.0010 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118537 restraints weight = 26113.442| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.39 r_work: 0.3623 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15752 Z= 0.117 Angle : 0.592 10.260 21549 Z= 0.310 Chirality : 0.041 0.204 2322 Planarity : 0.004 0.044 2602 Dihedral : 14.287 60.183 2436 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 3.29 % Allowed : 21.64 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1758 helix: 1.74 (0.19), residues: 746 sheet: 1.45 (0.30), residues: 250 loop : -0.26 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 628 TYR 0.014 0.001 TYR A1166 PHE 0.018 0.001 PHE A 197 TRP 0.027 0.001 TRP A 175 HIS 0.003 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (15751) covalent geometry : angle 0.59230 / 0.31 (21547) SS BOND : bond 0.00271 / 0.14 ( 1) SS BOND : angle 0.45433 / 0.26 ( 2) hydrogen bonds : bond 0.04106 / 2.86 ( 733) hydrogen bonds : angle 4.37424 / 3.10 ( 1999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 356 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: A 877 MET cc_start: 0.7479 (mmm) cc_final: 0.7262 (mmt) REVERT: B 134 LYS cc_start: 0.8335 (tptp) cc_final: 0.8098 (tttp) REVERT: B 158 GLN cc_start: -0.2933 (OUTLIER) cc_final: -0.3541 (mt0) REVERT: B 310 GLU cc_start: 0.8005 (mp0) cc_final: 0.7566 (mp0) REVERT: C 86 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6553 (mm) outliers start: 51 outliers final: 27 residues processed: 391 average time/residue: 0.6003 time to fit residues: 258.3033 Evaluate side-chains 371 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 341 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 137 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 400 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.122972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114628 restraints weight = 26199.925| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.40 r_work: 0.3562 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 15752 Z= 0.215 Angle : 0.714 10.047 21549 Z= 0.375 Chirality : 0.047 0.192 2322 Planarity : 0.006 0.054 2602 Dihedral : 14.446 62.507 2436 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 4.39 % Allowed : 20.74 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1758 helix: 1.34 (0.19), residues: 753 sheet: 1.23 (0.31), residues: 238 loop : -0.40 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 628 TYR 0.018 0.002 TYR A 649 PHE 0.024 0.002 PHE A 197 TRP 0.025 0.002 TRP A 175 HIS 0.007 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (15751) covalent geometry : angle 0.71441 / 0.38 (21547) SS BOND : bond 0.00635 / 0.33 ( 1) SS BOND : angle 0.91251 / 0.51 ( 2) hydrogen bonds : bond 0.05748 / 3.99 ( 733) hydrogen bonds : angle 4.72613 / 3.35 ( 1999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 345 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: A 877 MET cc_start: 0.7536 (mmm) cc_final: 0.7313 (mmt) REVERT: B 134 LYS cc_start: 0.8381 (tptp) cc_final: 0.8145 (tttp) REVERT: B 158 GLN cc_start: -0.2986 (OUTLIER) cc_final: -0.3574 (mt0) REVERT: C 86 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6588 (mm) outliers start: 68 outliers final: 39 residues processed: 393 average time/residue: 0.5790 time to fit residues: 250.5265 Evaluate side-chains 382 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 340 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1050 LYS Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 0.0870 chunk 46 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 120 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 404 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.125159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.116790 restraints weight = 26075.196| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.41 r_work: 0.3595 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15752 Z= 0.137 Angle : 0.644 11.817 21549 Z= 0.338 Chirality : 0.043 0.183 2322 Planarity : 0.005 0.045 2602 Dihedral : 14.368 61.210 2436 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 3.04 % Allowed : 21.96 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1758 helix: 1.44 (0.19), residues: 756 sheet: 1.44 (0.31), residues: 241 loop : -0.32 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1096 TYR 0.023 0.002 TYR A1166 PHE 0.018 0.001 PHE A 197 TRP 0.033 0.001 TRP A 175 HIS 0.003 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (15751) covalent geometry : angle 0.64432 / 0.34 (21547) SS BOND : bond 0.00337 / 0.18 ( 1) SS BOND : angle 0.47241 / 0.27 ( 2) hydrogen bonds : bond 0.04649 / 3.23 ( 733) hydrogen bonds : angle 4.58400 / 3.26 ( 1999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 350 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: A 877 MET cc_start: 0.7474 (mmm) cc_final: 0.7254 (mmt) REVERT: A 1145 ASP cc_start: 0.7601 (m-30) cc_final: 0.7396 (m-30) REVERT: B 134 LYS cc_start: 0.8372 (tptp) cc_final: 0.8132 (tttp) REVERT: B 158 GLN cc_start: -0.3089 (OUTLIER) cc_final: -0.3656 (mt0) REVERT: B 310 GLU cc_start: 0.8006 (mp0) cc_final: 0.7575 (mp0) REVERT: C 86 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6574 (mm) outliers start: 47 outliers final: 31 residues processed: 387 average time/residue: 0.5877 time to fit residues: 250.2691 Evaluate side-chains 378 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 8 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 564 GLN A 736 ASN A 843 GLN A 922 GLN A1175 GLN B 195 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 355 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.117058 restraints weight = 26301.315| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.41 r_work: 0.3600 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15752 Z= 0.136 Angle : 0.642 10.967 21549 Z= 0.336 Chirality : 0.043 0.171 2322 Planarity : 0.005 0.044 2602 Dihedral : 14.336 60.918 2436 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 2.71 % Allowed : 22.48 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1758 helix: 1.50 (0.19), residues: 755 sheet: 1.36 (0.31), residues: 243 loop : -0.30 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 203 TYR 0.023 0.002 TYR A1166 PHE 0.019 0.001 PHE A 197 TRP 0.043 0.001 TRP A 175 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (15751) covalent geometry : angle 0.64173 / 0.34 (21547) SS BOND : bond 0.00334 / 0.18 ( 1) SS BOND : angle 0.48518 / 0.28 ( 2) hydrogen bonds : bond 0.04528 / 3.15 ( 733) hydrogen bonds : angle 4.53708 / 3.23 ( 1999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 355 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: A 877 MET cc_start: 0.7495 (mmm) cc_final: 0.7276 (mmt) REVERT: B 134 LYS cc_start: 0.8356 (tptp) cc_final: 0.8118 (tttp) REVERT: B 158 GLN cc_start: -0.3004 (OUTLIER) cc_final: -0.3580 (mt0) REVERT: B 310 GLU cc_start: 0.8018 (mp0) cc_final: 0.7588 (mp0) REVERT: C 86 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6551 (mm) outliers start: 42 outliers final: 30 residues processed: 386 average time/residue: 0.5603 time to fit residues: 238.4169 Evaluate side-chains 378 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 345 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 5 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 564 GLN A 736 ASN A 843 GLN A 922 GLN A1157 ASN A1175 GLN B 195 ASN B 261 GLN B 355 GLN B 400 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.124403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116016 restraints weight = 26049.565| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.41 r_work: 0.3584 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15752 Z= 0.163 Angle : 0.668 10.808 21549 Z= 0.350 Chirality : 0.044 0.170 2322 Planarity : 0.005 0.043 2602 Dihedral : 14.383 61.577 2436 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.92 % Favored : 96.02 % Rotamer: Outliers : 3.29 % Allowed : 22.22 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1758 helix: 1.41 (0.19), residues: 754 sheet: 1.39 (0.30), residues: 241 loop : -0.37 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 203 TYR 0.023 0.002 TYR A1166 PHE 0.021 0.002 PHE A 197 TRP 0.046 0.002 TRP A 175 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (15751) covalent geometry : angle 0.66797 / 0.35 (21547) SS BOND : bond 0.00492 / 0.26 ( 1) SS BOND : angle 0.64966 / 0.37 ( 2) hydrogen bonds : bond 0.04972 / 3.46 ( 733) hydrogen bonds : angle 4.62186 / 3.28 ( 1999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6346.95 seconds wall clock time: 108 minutes 37.14 seconds (6517.14 seconds total)